6KM9

Crystal structure of SucA from Vibrio vulnificus

• PDB DOI: https://doi.org/10.2210/pdb6KM9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-31 Released: 2020-08-05 
• Deposition Author(s): Seo, P.W., Kim, J.S.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.249 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin.

Seo, P.W., Jo, H.J., Hwang, I.Y., Jeong, H.Y., Kim, J.H., Kim, J.W., Lee, E.Y., Park, J.B., Kim, J.S.

(2020) Catal Sci Technol 

• DOI: https://doi.org/10.1039/C9CY01566C

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 200.54 kDa 
• Atom Count: 13,577 
• Modelled Residue Count: 1,689 
• Deposited Residue Count: 1,772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component	A, B	886	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: sucA, VV1_0157 EC: 1.2.4.2
UniProt
Find proteins for A0A3Q0L1E1 (Vibrio vulnificus (strain CMCP6)) Explore A0A3Q0L1E1  Go to UniProtKB:  A0A3Q0L1E1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	E [auth A], I [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
P6G	C [auth A], G [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.249 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.271	α = 90
b = 76.708	β = 100.56
c = 144.579	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Seo, P.W., Kim, J.S.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description